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Good day, The location of indels can be retrieved from a PairwiseAlignmentsSingleSubject object by using indel. Determining any difference between the two sequences, including substitutions, is not quick nor easy. I suppose that summary displays details of the mismatches, but the variable is of class PairwiseAlignmentsSingleSubjectSummary which has no documented acces...

...[i,1]) # get gene id tmp.subject<-as.vector(genebody[i,2]) # get gene sequence tmp.exons<-exons[which(exons[,1]==tmp.id),] # get exons of the selected genes tmp.pattern<-as.vector(tmp.exons[,3]) # define exons as patterns for alignment tmp.align<-pairwiseAlignment(pattern=tmp.pattern, subject=tmp.subject,type="local") # align all exons pairwise to gene sequence tmp.start<-start(subject(tmp.align)) # vector of all alignment starts tmp.end<-end(subject(tmp.align)) # vector of all alignment ends for(ex in 1:(length(...

...uire(stringr) # library(help=stringr) all.seqS <- str_replace(seqS4,"-" , "") # how do we allign this? data.frame(Real_sequence = seqS4, The_sequence_we_see = all.seqS) I understand that if all I had was a string and a pattern I would be able to use library(Biostrings) pairwiseAlignment(...) But in the case I present we are dealing with many sequences to align to one another (instead of aligning them to one pattern). Is there a known method for doing this in R? Thanks, Tal ----------------Contact Details:------------------------------------------------------- Contact...